Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection

Publikationstyp:
Zeitschriftenaufsatz
Metadaten:
Autoren
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000373079900002&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.4137/EBO.S30902
Externe Identifier
  • Clarivate Analytics Document Solution ID: DH8XJ
  • PubMed Identifier: 26819542
ISSN
1176-9343
Zeitschrift
EVOLUTIONARY BIOINFORMATICS
Schlüsselwörter
  • branch-site test
  • PAML
  • dN/dS
  • positive selection
  • molecular evolution
Paginierung
11 - 17
Datum der Veröffentlichung
2015
Status
Published
Titel
Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection
Sub types
  • Article
Ausgabe der Zeitschrift
11

Datenquelle: Web of Science (Lite)

Andere Metadatenquellen:
Abstract
<jats:p>The branch-site test of positive selection is a standard approach to detect past episodic positive selection in a priori-specified branches of a gene phylogeny. Here, we ask if differences in the topology of the gene tree have any influence on the ability to infer positively selected sites. Using simulated sequences, we compare the results obtained for true and rearranged topologies. We find a strong relationship between “conflicting branch length,” which occurs when the set of sequences that experiences selection for a given topology and foreground is changed, and the ability to predict positively selected sites. Moreover, by reanalyzing a previously published data set, we show that the choice of a gene tree also affects the results obtained for real-world sequences. This is the first study to demonstrate that tree topology has a clear effect on the inference of positive selection. We conclude that the choice of a gene tree is an important factor for the branch-site analysis of positive selection.</jats:p>
Autoren
DOI
10.4137/ebo.s30902
eISSN
1176-9343
ISSN
1176-9343
Zeitschrift
Evolutionary Bioinformatics
Sprache
en
Online publication date
2016
Paginierung
EBO.S30902 - EBO.S30902
Datum der Veröffentlichung
2015
Status
Published
Herausgeber
SAGE Publications
Herausgeber URL
http://dx.doi.org/10.4137/ebo.s30902
Datum der Datenerfassung
2022
Titel
Gene Tree Affects Inference of Sites under Selection by the Branch-Site Test of Positive Selection
Ausgabe der Zeitschrift
11s2

Datenquelle: Crossref

Abstract
The branch-site test of positive selection is a standard approach to detect past episodic positive selection in a priori-specified branches of a gene phylogeny. Here, we ask if differences in the topology of the gene tree have any influence on the ability to infer positively selected sites. Using simulated sequences, we compare the results obtained for true and rearranged topologies. We find a strong relationship between "conflicting branch length," which occurs when the set of sequences that experiences selection for a given topology and foreground is changed, and the ability to predict positively selected sites. Moreover, by reanalyzing a previously published data set, we show that the choice of a gene tree also affects the results obtained for real-world sequences. This is the first study to demonstrate that tree topology has a clear effect on the inference of positive selection. We conclude that the choice of a gene tree is an important factor for the branch-site analysis of positive selection.
Addresses
  • Instituto Gulbenkian de Ciência, Oeiras, Portugal.; Programa de Doutoramento em Biologia Computational (PDBC), Instituto Gulbenkian de Ciência, Oeiras, Portugal.
Autoren
DOI
10.4137/ebo.s30902
eISSN
1176-9343
Externe Identifier
  • PubMed Identifier: 26819542
  • PubMed Central ID: PMC4718152
Open access
true
ISSN
1176-9343
Ausgabe der Veröffentlichung
Suppl 2
Zeitschrift
Evolutionary bioinformatics online
Sprache
eng
Medium
Electronic-eCollection
Online publication date
2016
Open access status
Open Access
Paginierung
11 - 17
Datum der Veröffentlichung
2015
Status
Published
Datum der Datenerfassung
2016
Titel
Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection.
Sub types
  • research-article
  • Journal Article
Ausgabe der Zeitschrift
11

Files

https://journals.sagepub.com/doi/pdf/10.4137/EBO.S30902 https://europepmc.org/articles/PMC4718152?pdf=render

Datenquelle: Europe PubMed Central

Abstract
The branch-site test of positive selection is a standard approach to detect past episodic positive selection in a priori-specified branches of a gene phylogeny. Here, we ask if differences in the topology of the gene tree have any influence on the ability to infer positively selected sites. Using simulated sequences, we compare the results obtained for true and rearranged topologies. We find a strong relationship between "conflicting branch length," which occurs when the set of sequences that experiences selection for a given topology and foreground is changed, and the ability to predict positively selected sites. Moreover, by reanalyzing a previously published data set, we show that the choice of a gene tree also affects the results obtained for real-world sequences. This is the first study to demonstrate that tree topology has a clear effect on the inference of positive selection. We conclude that the choice of a gene tree is an important factor for the branch-site analysis of positive selection.
Date of acceptance
2015
Autoren
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/26819542
DOI
10.4137/EBO.S30902
Externe Identifier
  • PubMed Central ID: PMC4718152
ISSN
1176-9343
Ausgabe der Veröffentlichung
Suppl 2
Zeitschrift
Evol Bioinform Online
Schlüsselwörter
  • PAML
  • branch-site test
  • dN/dS
  • molecular evolution
  • positive selection
Sprache
eng
Country
United States
Paginierung
11 - 17
PII
ebo-suppl.2-2015-011
Datum der Veröffentlichung
2015
Status
Published online
Datum, an dem der Datensatz öffentlich gemacht wurde
2016
Titel
Gene Tree Affects Inference of Sites Under Selection by the Branch-Site Test of Positive Selection.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
11

Datenquelle: PubMed

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